Firstly, what Itachi said back then was only hype for Jiraiya.
Secondly, Itachi was a double-agent i.e. liar, so he could've lied about Jiraiya's power, so it seemed to Kisame that Jiraiya was stronger, thereby preventing a fight.
Thirdly, this was said way back in the series when Kishi didn't think about SM or Susanoo.
Anyone who has followed the manga till both of their respective deaths must know that MS Itachi is undoubtedly stronger than SM Jiraiya.
And just because Imperfect Sage Mode itself is inferior to Perfect Sage Mode doesn't mean the corresponding user is also inferior. Sage Mode is just an upgraded state, not an arsenal of power. So that itself doesn't prove Naruto is stronger than Jiraiya.
Also, SM Naruto
directly said that he < MS Sasuke.
MS Sasuke > SM Naruto pre war arc.
And hypothetical War Arc MS Sasuke > War Arc SM Naruto.